Thursday, February 27, 2014

Richard Dawkins: How Could Anyone “Possibly Doubt the Fact of Evolution”

The Single Most Convincing Fact

Evolutionists like to say that there are mountains of evidence for evolution, but what is the best evidence? What would make a creationist think twice? Twenty five seconds into this video evolutionist Richard Dawkins answers this question. His killer evidence is the congruence between the genes of different plants and animals. Compare the genes across a range of species and you’ll see a “perfect hierarchy, a perfect family tree.” In fact, you’ll see the same result for evolutionary trees using just single genes—the so-called gene trees. It works “with every gene you do separately.”

[0.25] I think perhaps the single most convincing fact—observation—you could point to would be the pattern of resemblances that you see when you compare the genes, using modern DNA techniques, such as looking at the letter-to-letter correspondences between the genes—compare the genes of any pair of animals you like—a pair of animals or a pair of plants—and then plot out the resemblances and they fall in a perfect hierarchy, a perfect family tree. … [1.05] Moreover the same thing works with every gene you do separately and even pseudogenes that don’t do anything but are vestigial relics of genes that once did something. I find it extremely hard to imagine how any creationist that actually bothered to listen to that, could possibly doubt the fact of evolution.

Dawkins went on to have some rather harsh words for creationists. The message was clear. The evidence for evolution falls perfectly into place. It makes evolution a fact that is beyond any reasonable doubt. And anyone who doubts this is a bad person.

This sentiment is by no means particular to Dawkins. I have heard this same claim, and others like it, dozens of times. Sometimes informally in lectures, discussions, debates and so forth. Other times in textbooks or other literature.

What is amazing is the evolutionist’s high confidence and self-assuredness in such a blatant misrepresentation of science. It would be difficult to imagine a bigger falsehood. Phylogenetic incongruence is rampant in evolutionary studies. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many. These incongruences are caused by just about every kind of contradiction possible. Molecular sequences in one or a few species may be out of place amongst similar species. Or sequences in distant species may be strangely similar. As one paper admitted, there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”

An even more severe problem is that in many cases no comparison is even possible. The molecular sequence is found in one species but not its neighbors. When this problem first became apparent evolutionists thought it would be resolved as the genomes of more species were decoded. No such luck—the problem just became worse. Not surprisingly evolutionists carefully prefilter their data. As one paper explained, “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”

Short genes that produce what are known as microRNA also contradict Dawkins’ high claim. In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.”

Another paper admits that “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.”

And yet in public presentations of their theory, evolutionists present a very different story. As Dawkins explained, gene comparisons “fall in a perfect hierarchy, a perfect family tree.” This statement is so false it isn’t even wrong—it is absurd. And then Dawkins chastises anyone who “could possibly doubt the fact of evolution.” Unfortunately this sentiment is typical. Evolutionists have no credibility.

315 comments:

From WikiPedia "The Big Lie (German: Große Lüge) is a propaganda technique. The expression was coined by Adolf Hitler, when he dictated his 1925 book Mein Kampf, about the use of a lie so "colossal" that no one would believe that someone "could have the impudence to distort the truth so infamously." Hitler asserted the technique was used by Jews to unfairly blame Germany's loss in World War I on German Army officer Erich Ludendorff."

It was said of Hitler: "His primary rules were: never allow the public to cool off; never admit a fault or wrong; never concede that there may be some good in your enemy; never leave room for alternatives; never accept blame; concentrate on one enemy at a time and blame him for everything that goes wrong; people will believe a big lie sooner than a little one; and if you repeat it frequently enough people will sooner or later believe it"

Evolutionism posits a somewhat gradual, incremental evolution driven by culled genetic accidents. Natural selection, a process of elimination, is said to be blind, mindless and incorporates heritable random, as in happenstance/ accidental, mutations. Dawkins calls it blind watchmaker evolution.

What we need is a way to model what mutations do. That is something beyond the piddly changes we observe. Changes in beak size does not explain the finch. Anti-biotic resistance does not explain bacteria. Moth coloration does not explain the moth. Changes in eye color does not explain the vision system nor the type of eye nor the organism. An albino dwarf with sickle-celled anemia is what we can get when mutations accumulate. Not quite what evolutionism requires.

We need to be able to test the hypothesis that changes to genomes can account for the diversity of life starting from the first populations as Darwin saw it- simple prokaryotes. Only then could we determine if natural selection is up to the task. But thanks to the current state of biology being dominated by blind watchmaker evolution, no one has any idea what makes an organism what it is and the evidence is against the “organisms are the sum of their genome”*

You would think that answering that question what makes an organism what it is? (with science as opposed to dogmatic declaration) with be paramount to biology. Because without an answer to that question evolutionism is untestable and Dobzhansky is just question begging "Nothing in biology makes sense except in the light of evolution".

And that is another reason why Doug Theobald's "29+ evidences for macroevolution" is absent a mechanism and also why it fails-> there aren't any known mechanisms for producing macroevolutionary change because no one even knows what it entails.

* we are just what emerges from the somehow coordinayed interactions of the matter and energy of a fertilized egg (the environemnet wouldn’t change what type of organism comes out)

Yoconodon is the supposed missing link for reptilian lower jaws evolving into the mammalian inner ear. It is the only mammal among the therians to have menkels cartilage attaching the ear ossicles to the jaw. Part of this claim is based on recapitulation theory, or otegeny recapitulates phylogeny. As Natures states regarding Liaoconodon hui "the embryonic pattern of modern mammals recapitulates the phylogenetic changes". Recapitulation was abandon a very long time ago. Studies in otogeny have disproven this as early as 1922. There is no actual proof the mammalian ear bones were evolve from reptilian lower jawbones, which are connected by ossified Menkels cartilage.

The problem with the alleged evolution of the mammalian inner ear is there isn't any genetic link. Zachriel talks as if it is all Lamarkian, ie acquired traits that gets passed down. They definitely never speak of any genetic connection to the alleged transformations.

Quite true. The Meckels cartilage provide the shape for the ear and jaw, then is absorbed, during development. The processes are totally different. In the case of Yanoconodon the problem is either the animal has devolved or the ear would have had to evolve twice. This strains credulity.

What I don't understand is how the mammalian ear could have evolved from a repilian jaw bone without some sort of teleology. The bones have to be in the correct position and have the correct shape in order to work as an ear. How did the jaw bones know what shape they needed to take, and where to go?

First of all it's not a transition to anything, as the Nature article points out. It could be a case of arrested development. The ear bones a mammalian in order to function need a host of other systems to function. It's a long way from reptilian rear jawbone pieces to a mammalian ear. In reptiles the meckels cartilage ossifies to form part of the jaw. Simply having a mammal that has a piece of meckels cartilage attached to the ear bone is not sufficient to prove the reptile jaw evolved to an ear. That's ad hoc. Neither are the claims regarding the reptile, Liaoconodon hui, which has a piece of ossified meckels cartilage attached form the jaw to the ear. So what? Unless you have a complete sequence showing the development you can't say anything definitive. (At this point you will protest "we can't expect that!" You're right we can't. But without it all you've got is a just so story.)

Now if you cannot prove your claims from the fossil record you'll have to find another way. Besides postulating disproven recapitulation theories. (Which goes to show what happens when you lie to students about "proofs". But I digress.) Neo-Darwinians had claimed advances in genetic information would solve the problem. It has made it worse. It has shown the incremental micro-mutational model to be totally wrong. So now evolutionary biologist are scrambling for another explanation. And we're back to punctuated equilibrium, evo-devo, ect. Everything old is new. If you find this convincing fine. To me it's too vague to mean anything.

The adaptation is believed to be paedomorphic. Small changes in timing during development, heterochrony, led to a series of selectable changes. See Ji et al., Evolutionary development of the middle ear in Mesozoic therian mammals, Science 2009.

eklektos: First of all it's not a transition to anything, as the Nature article points out.

The word "Nature" shows up only once before on this page, when you seemed confused about recapitulation. If you are referring to Jin et al. 2011, then "transition" is right in the title of the article, "Transitional mammalian middle ear from a new Cretaceous Jehol eutriconodont".

eklektos: It's a long way from reptilian rear jawbone pieces to a mammalian ear.

This discussion concerns the evolution of auditory ossicles.

eklektos: Simply having a mammal that has a piece of meckels cartilage attached to the ear bone is not sufficient to prove the reptile jaw evolved to an ear.

It was predicted. Lucky guess?

eklektos: Now if you cannot prove your claims from the fossil record you'll have to find another way.

We also have the evidence from embryonic development, which actually came first, and was used to predict the fossil evidence. Lucky guess?

Zachriel:The adaptation is believed to be paedomorphic. Small changes in timing during development, heterochrony, led to a series of selectable changes. See Ji et al., Evolutionary development of the middle ear in Mesozoic therian mammals, Science 2009.

I think they found what they were looking for. But on it's own it has no explanatory power. Stop pretending that evolutionary biologist think the fossil record is sufficient. They say all the time it's not. It's in their textbooks.

The word "Nature" shows up only once before on this page, when you seemed confused about recapitulation. If you are referring to Jin et al. 2011, then "transition" is right in the title of the article, "Transitional mammalian middle ear from a new Cretaceous Jehol eutriconodont".

That's because you only read the abstract. It's in the article, not the abstract.

This discussion concerns the evolution of auditory ossicles.

I said: For those interested in the problems with reptile to mammalian inner ear development

We also have the evidence from embryonic development, which actually came first, and was used to predict the fossil evidence. Lucky guess?

You don't, sorry. Unless you wish to posit recapitulation. Is that you're argument?

depends on what Zachriel is referring to. If all he's referring to the Yanoconodon having a mengels cartilage attached to the ear It's banal and vague. I could predict practically anything could be found somewhere in nature. Monotremes have menkels cartilage attached until full maturity, so it's not unique in mammals.

First it's a generic and banal "prediction", and it's not even unique. Monotremes retain meckels cartilage till maturity. Further if your reasoning from embryology then whole starting point is false. Recapitulation is a false theory. Even Darwinist for the most part have abandon it. Developmental Biologist have abandon it virtually in Toto. (There always may be a few fringe folks out there.)

Second read the blinkin article, that's where they hedge their bets and modify their claims. Nature is the name of the publication. I cited it because that was the publication the came from so you're confused.

I'll get to the nonsense about apes and humans later. Also when we are talking of peripheral systems we a talking of trivial changes. Like coloring, expression of feature, etc. Not major morphological changes.

In the case of Liaoconodon hui it cannot be transitional, the ear already existed in Hadrocodium. The DDME is 40 Ma and 75 Ma years earlier. So it's reverse evolution? As to Yanoconodon there could be any number of reasons it had meckels cartilage connectin the jaw to the ear bones. Birth defect, some functional use, not fully developed. (like montremes), given where it came from it could be a fraud. And even if genuine we would have to have tissue to make any sort of judgment about it.

Black-and-white thinking. While organisms don't go through all the stages of their evolutionary history, they do show many aspects of their evolutionary history. We've mentioned this before.

eklektos: Second read the blinkin article, that's where they hedge their bets and modify their claims.

We have. You said the article said it's not a transitional. That is contrary to what the article actually says.

eklektos: In the case of Liaoconodon hui it cannot be transitional, the ear already existed in Hadrocodium.

"A transitional fossil is any fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group."

eklektos: I could predict practically anything could be found somewhere in nature.

But you didn't, and you don't. Liaoconodon supports the Reichert–Gaupp theory, based on embryological evidence more than a century ago. At that time, it seemed incredible to support that jaw bones could evolve into ossicles, how both functions could be served while providing a selective advantage. Since then, a series of fossils show not only that it could happen, but that it did.

""natschuster: How many predictions did evolutionists make that turned out wrong?"

Tons. Which means those hypotheses were discarded as unsupported or falsified.

"natschuster: If there are a lot of wrong predictions, then this one is just a lucky guess."

You're saying it was a lucky guess? Should we look at some other transitionals?"

If most predictions mde by evolutionists turn out to be false, then the few correct ones may very well be lucky guesses. And by transitionals, do you mean things like IDA or tiktaalik? Turns out hthose aren't the real transitionals, they just hva something like a transitional condition, The real transitionals are still unfound, so I;m not sure how accurately the predictions turned out. I'd only give half credit.

natschuster: If most predictions mde by evolutionists turn out to be false, then the few correct ones may very well be lucky guesses.

So, paleontologists mount an expedition to the Canadian arctic, spend years looking in the rocks, and just happen to stumble across a fishapod with the exact characteristics they had predicted? Just a lucky guess?

"A transitional fossil is any fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group."

Of related note: Richard Dawkins claimed that the FOXP2 gene was among ‘the most compelling evidences’ for establishing that humans evolved from monkeys, yet, as with all the other evidences offered from Darwinists, once the FOXP2 gene was critically analyzed it fell completely apart as proof for human evolution:

In the following paper, the paper admits that the FOXP2 gene evidence (i.e. Dawkins' 'best' evidence) is ‘tenuous’,,

Human brain evolution: From gene discovery to phenotype discovery - Todd M. Preuss - February 2012 Excerpt: It is now clear that the genetic differences between humans and chimpanzees are far more extensive than previously thought; their genomes are not 98% or 99% identical.,,, ,,our understanding of the relationship between genetic changes and phenotypic changes is tenuous. This is true even for the most intensively studied gene, FOXP2,, In part, the difficulty of connecting genes to phenotypes reflects our generally poor knowledge of human phenotypic specializations, as well as the difficulty of interpreting the consequences of genetic changes in species that are not amenable to invasive research. http://www.pnas.org/content/109/suppl.1/10709.full.pdf

As well, the primary piece of evidence, at the Dover trial, trying to establish chimp human ancestry from SNP (Single Nucleotide Polymorphism) evidence was overturned:

Dover Revisited: With Beta-Globin Pseudogene Now Found to Be Functional, an Icon of the “Junk DNA” Argument Bites the Dust - Casey Luskin - April 23, 2013http://www.evolutionnews.org/2013/04/an_icon_of_the_071421.html

These ideas were subsequently championed by Stephen Jay Gould, in his book Ontogeny and Phylogeny, who emphasized that the phenotypic consequences of gene-expression changes would be magnified if they occurred early in development. These writings established the expectation that we should be able to discover a few key genetic changes that account for many, if not most, of the phenotypic differences between humans and chimpanzees.

These are the very type of claims for which Gould was pummeled by Neo-Darwinists. The higher order developmental regulatory gene networks are the very ones that you cannot incrementally vary without catastrophic results. And these are the only ones that could affect major changes in body plans. So I guess we are back to punctuated equilibrium.

Tio the best of my knowledge, they changed the hox genes in fruit flies in every coceivable way. The only results were defective fruit flies, or dead fruit flies. The evidence seems to be against evo-devo. (Did I say it right?)

eklektos: The higher order developmental regulatory gene networks are the very ones that you cannot incrementally vary without catastrophic results.

It's not a simple dichotomy. Regulatory networks are complex and multifaceted. While adding a new pair of limbs would probably not be advantageous, a lengthening of the legs, or an increase in the brain case, might.

Peripheral changes to the regulatory networks will change the upholstery color, they will not make major changes to body plan. These regulatory networks are hierarchical. The peripheral networks are also downstream in development. You can change downstream components because body plan has already been realized. If you change upstream components you get catastrophic failures. If you wish to study this further I suggest you read Eric Davidsons "Evolutionary bioscience as regulatory systems biology":

http://www.sciencedirect.com/science/article/pii/S0012160611000911

If you really want to get to the meat of it get his textbook but be prepared for a slog.

Also your claim doesn't really say anything. It is too general to address the issue. Almost 100 years of directed mutagenic studies have shown that altering early developmental networks has catastrophic effects on the organism. But these are the very ones that must be changed for macroevolution to be possible. Even further upstream are the epigenetic factors that control cell arrangement and 3 dimensional symmetry. Again, altering these has catastrophic effects. These systems contain specified complexity. They cannot be changed in an incremental fashion. Any changes must be global and specific.

"It's not a simple dichotomy. Regulatory networks are complex and multifaceted. While adding a new pair of limbs would probably not be advantageous, a lengthening of the legs, or an increase in the brain case, might."

Ok, but you do not know which of that changes wold be advantaeous and neither "evolution" (whatever it is know" so life forms should be trying that change regularly. And we do not see that.

Peripheral changes are all that separates humans from other apes. Guess that's not macroevolutiony enough for you.

Did you just miss the whole discussion of the difference between apes and humans? The differences are not trivial. Apes have different structures at a lot of levels. Hips, feet, hands, nasal cavities, etc. As to the problems with the fusion argument, which touches upon this see:

If you are talking about Precambrian tube worms, then regulatory genes are not so downstream, and a lateral protuberance can be quite an advantage.

A. You don't have any genetic information on pre-Cambrian tube worm. B. Even in a bacteria it won't work because complex molecular machinery like the flagellar motor cannot be assembled piecemeal.

"a pair of ragged claws Scuttling across the floors of silent seas."

Poetic.

That's not plausible. Perhaps you mean every single-point mutation has been tried. That's quite a different statement.

Actually they mutated several sights. Besides, if the changes are incremental as Neo-Darwinist claim then it would be single-point, or at the most a two base pair mutation. See the Axe study. Ignore his statement about ID. Look at the population genetics.

Cornelius:What would make a creationist think twice?Thank you. That question will keep a smile on my face for the entire day, along with the echoes of decades worth of conversations with creationists. (Hint: the answer to the question rhymes with "nothing".)

Thank you. That question will keep a smile on my face for the entire day, along with the echoes of decades worth of conversations with creationists. (Hint: the answer to the question rhymes with "nothing".)

Quelle surprise! Closely related bats are hard to tell apart! Notice they provide a number of plausible mechanisms for the incongruence, such as saturation of molecular substitutions.

Cornelius Hunter: As one paper admitted, there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.”

That doesn't impact the phylogenetic tree.

Cornelius Hunter: Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”

It's called convergent evolution, which is important evidence for evolutionary theory. See Darwin 1859.

As for the particulars, prestin is a motor protein involved in high frequency hearing. Bats and whales both evolved echolocation, which involves ultrasonic sound, so the genes converged on the same solution. If you only include synonymous changes, the genes support the standard phylogenetic tree.

Cornelius Hunter: In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found “a single example that would support the traditional tree.”

Misleading. The question doesn't concern the overall tree, but resolving relationships within Eutheria, which diverged rather rapidly.

Well, not perfect, but strongly supported. ... Quelle surprise! Closely related bats are hard to tell apart! Notice they provide a number of plausible mechanisms for the incongruence, such as saturation of molecular substitutions. ... That doesn't impact the phylogenetic tree. ... It's called convergent evolution, which is important evidence for evolutionary theory. See Darwin 1859. ... As for the particulars, prestin is a motor protein involved in high frequency hearing. Bats and whales both evolved echolocation, which involves ultrasonic sound, so the genes converged on the same solution. If you only include synonymous changes, the genes support the standard phylogenetic tree. ... Misleading. The question doesn't concern the overall tree, but resolving relationships within Eutheria, which diverged rather rapidly.

Again, why don't you remind us exactly which philosophy of science you subscribe to? Oh that's right, you refuse to rigorously defined the term, despite being asked to over and over and over again.

From a previous comment…

01. Predictions of scientific theories are not prophecy. Unlike a supposed omnipotent being, they cannot take into account all parallel yet unrelated events or effects that might effect the outcome. This sort of expectation is unreasonable as it ignores progress we've made in the field of epistemology.

02. We do not falsify theories, in practice, until we come up with an explanation for unexpected outcomes. This is because observations are themselves theories about what happened in a particular time and place. A concrete example of this was supposed observations of neutrinos traveling faster than the speed of light during the OPERA experiment in 2011. Despite the fact that we received unexpected results, we did not falsify Einstein's theory because we did not yet have a better explanation for the results. Specifically, we had no explanation as to why the particular neutrinos in the OPERA experiment traveled faster than other neutrinos tested in other experiments. Eventually, we did find an explanation as to why the prediction was not met: an incorrectly attached fiber optic cable and a timer with a clock ticking too quickly.

03. We have an explanation for why results varied in the case of yeast cells: horizontal gene transfer. Furthermore, we expect our theories to be incomplete and contain errors by nature of staring out as a conjectures. As such, we expect to discover new means of variations, such as HGT, in the future.

Human knowledge grows when we start with a problem, conjecture theories of how to solve them, criticize these theories and discard errors we find. That's how we make progress.

Yet you objections here seem to think that's not how science works. Apparently, science “works” in what ever way is most convenient for your “argument” at the moment you happen to make it.

So, if anything, we’re NOT willfully blind to this sort of hand waving. That's the chorus your preaching to.

J: It's no longer willful. He's practiced obfuscation so long he is utterly irrational. He actually argued to me that you can deduce implications from premises with undefined terms. Amazing, indeed. One can not conceive of a greater degree of confusion.

Jeff: He actually argued to me that you can deduce implications from premises with undefined terms.

Z: Um, no. We ...

J: Are you demon possessed or do you have a mouse in your pocket?

Z: said that the Law of Non-Contradiction only applies when the dichotomy is well-defined.

J: Then get off your lazy posterior and define matter and Einstein's space once and for all. How can you claim to be communicating when you refuse to define your terms? You're either profoundly confused or utterly immoral (or both).

Z: said that the Law of Non-Contradiction only applies when the dichotomy is well-defined.

J: Where the LNC doesn't imply, no deductions are possible. The terms in a proposition have to be defined to imply anything specific and, therefore, testable. So if scientific hypotheses need to be testable, they have to be subject to the constraints of classical logic. If they don't need to be testable, just say so, and I'll inform your fellow fideists of the worthlessness of their religion.

Z: Um, no. We said that the Law of Non-Contradiction only applies when the dichotomy is well-defined.

J: Your examples, like "is it hot," etc, have nothing to do with the validity of the LNC. They have to do with the relativity of definitions--i.e., that individuals are diverse and therefore use similar words for non-identical experiences. But the LNC still applies to an individual's propositions given his/her own definitions, regardless of whether other individuals define the words in the proposition identically.

In short, the LNC applies to propositions whose terms are defined by the one who asserts the proposition. It matters not whether other people define the terms identically. But testers can't test the implications of hypotheses if the propositions that supposedly convey the meaning of the hypothetical theory consist of terms not similarly conceived of by those involved in testing the hypothesis.

The respective deductions differ when the propositional meaning is diversely conceived of by its interpreters. The LNC as a principle isn't undermined by this at all.

P.S. Define matter and Einstein's space so we can do the proper deductions from propositions that reference them.

Let me address another issue. Making statements like "He wasn't published by the scientific journals, he had to publish on his own." is nothing but ad hominem. Had Douglas Axe been willing to kowtow to the Darwinian establishment his work would have been heralded. All he would have had to do is use meaningless Neo-Darwinian jargon like "The results of this study shows the mechanisms of macro-evolutionary processes have not yet revealed how such a stunning complexity of organisms has arisen". He would have been accepted. But he looked at the data, said this won't work, and stood up for his principles. Good for him. The question is not how his paper got published. The question is were the methods he used sound and were the results of the study correct.

eklektos: Let me address another issue. Making statements like "He wasn't published by the scientific journals, he had to publish on his own." is nothing but ad hominem.

Sure. Of course ad hominem is not always a fallacy. In this case, though, it wasn't only not published in a mainstream journal, but he's the editor! The point of publication is to convince your peers. There's nothing necessarily wrong with self-publication.

eklektos: The question is were the methods he used sound and were the results of the study correct.

His conclusions were contradicted by the evidence before he wrote the paper. So there is that.

His conclusions were contradicted by the evidence before he wrote the paper. So there is that.

That's the issue under discussion, isn't it? You're assuming what you've yet to prove. Besides, the conclusions were actually couched in the same vague terms used in most papers. Design may be the best way to explain ..." As best I remember it. And they throw a hissy. Read the paper and critically think for yourself. Just like you uncritically read the Nature paper, well, if you read anything but the abstract, critically examine the arguments, try to find the flaws and don't just assume their correct. As to your ridiculous statement that I don't understand recapitulation, the quote from the paper by Meng himself is a classic definition of recapitulation theory, word for flippin word. As to the rest I'll address it later, got stuff to do.

THATS HIS BEST PIECE OF EVIDENCE!I will take this on.Wait. Is this scientific molecular evidence for mocular patterns being evidence of common descent and relationships?Its looks like a simple comparison and conclusion and in time for lunch.Its like saying HOW ELSE could something be AS evidence for how it came to be.This is mere reasoning on mere data.Even if right surely no one can argue its scientific research.Therefore another line of reasoning will slay it all.A creator used a basic model to allow diversity.A blueprint as he made in physics.Just as I would do.It should look as close alike as possible.It does as predicted.Evolution is false and can't possibly have scientific evidence behind it IF false.Another line of reasoning.

Joe G: If they do they wouldn't be objective and all levels and sets will be ill defined

That's easy to resolve statistically.

Zachriel: You do realize that the topology of a right-side up tree and an upside-down tree are the same?

Joe G: Do YOU realize that nested hierarchies are constructed from the top-down and trees of life from the bottom-up?

You really need to learn what is meant by topology.

http://www.chm.bris.ac.uk/motm/oec/images/tree.jpg

Joe G: And we are still waiting for the genetic evidence that supports the alleged evolution of the mammalian inner ear.

We already mentioned paeodomorphy and changes to developmental heterochrony. For a review, see Mallo, Formation of the Middle Ear: Recent Progress on the Developmental and Molecular Mechanisms, Developmental Biology 2001.

The simplest way would be to only include organisms that have a certain degree of similarity. In any case, extinction means there are usually discrete boundaries between taxa.

Joe G: So you don't understand what I said.

Sure we did. You said "nested hierarchies don't imply a tree, unless trees grow from the top down", then you said "Do YOU realize that nested hierarchies are constructed from the top-down and trees of life from the bottom-up?"

We provided you a tree of life that grows from the middle out, and we can provide another that grows from the bottom-up. A tree is an abstraction, and the topology of a right-side up tree and an upside-down tree are the same

CH: Dawkins went on to have some rather harsh words for creationists. The message was clear. The evidence for evolution falls perfectly into place. It makes evolution a fact that is beyond any reasonable doubt. And anyone who doubts this is a bad person.

It’s not perfect, but is strongly supported. If you demand perfection from the perspective of Empiricism, that *is* unreasonable because we’ve made progress since then.

Denying that we can and have made progress is, well, immoral. It’s a general purpose strategy that could be used to deny, well, anything. You just do not realize the moral implications of this sort of special pleading.

CH: Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits.

So let’s look at the supposed basis of Cornelius reasonable doubt? Why we can’t make progress in this area? What we have is failure by Cornelius to actually define what he means by science, which he changes when it is convenient for his purpose. This post is contains examples of just that….

CH: This paper reports on incongruent gene trees in bats.

Here, we have conflicts with the pattern, but we have explanations for those conflicts. So, theories are merely predictions to be observed, not explanations about how the world works, in reality.

CH: Or sequences in distant species may be strangely similar. As one paper admitted, there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.”

Here there are no observed conflicts with the tree pattern, but we currently lack an explanation for those specific conservations. Yet, this is supposedly a problem for the theory?

CH: Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”

No conflicts with the tree pattern here either. And we have an explanation: convergent evolution. Good ideas are good regardless of its source. Confused yet?

CH: Not surprisingly evolutionists carefully prefilter their data. As one paper explained, “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”

This is the very same paper, in which we have explanations for the conflicts! So, apparently, explaining things is filtering!

CH: In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.”

A traditional tree assumes that we learn nothing about how the rest of the world works, in reality. We’re back to science merely observing predictions, rather than actually explaining how the world works in reality.

That’s like saying we should have continued to criticize Newton’s theory with a “traditional” solar system which didn’t include Neptune. It’s setting the theory up to fail. No surprise here.

No wonder why Cornelius refuses to rigorously define what he means by science. Doing so would undermine the very objections he makes on a regular basis.

"With science one needs a way to test the claims made. With evolutionism there isn't any way to test its claims."

Evolutionists are quick to accuse those who disagree with them of not understanding the science or failing to define their terms, when in fact it is they who are using rubber rulers. Scott demands CH 'rigorously' define what he means by science, but no such definition is forthcoming from Scott.

Scott: "but we currently lack an explanation for those specific conservations."

So Scott, tell us how you know for sure such explanations are forthcoming? You accuse others of not being scientific in their approach, how is wishful thinking about future explanations scientific?

Cornelius is claiming that evolutionary theory isn't science, not me. As such, he's the one that needs to define what he means by science. Specifically, which specific philosophy of science he is referring to. In the absence of such a definition, his objections are merely a red herring.

For example, if, by science, Cornelius means logical positivism, then yes, evolutionary theory isn't science. But we have discarded logical positivism because it did not withstand criticism. From the wikipedia entry on the same…

After the Second World War's close in 1945, key tenets of logical positivism, including its atomistic philosophy of science, the verifiability principle, and the fact/value gap, drew escalated criticism. It was clear that empirical claims cannot be verified universally true.[12] Thus, as initially stated, the verifiability criterion made universal statements meaningless, and even made statements beyond empiricism for technological but not conceptual reasons meaningless, which would pose significant problems for science.[20][33][34] […] Even philosophers disagreeing among themselves on which direction general epistemology ought to take, as well as on philosophy of science, agreed that the logical empiricist program was untenable, and it became viewed as selfcontradictory.[35] The verifiability criterion of meaning was itself unverified.[35] Notable critics were Nelson Goodman, Willard Van Orman Quine, Norwood Hanson, Karl Popper, Thomas Kuhn, J L Austin, Peter Strawson, Hilary Putnam, and Richard Rorty.

All I have to do is point out that there are many philosophies of science. As such, it’s unclear exactly how his objections are relevant without disclosing exactly which philosophy he is referring to. He has yet to do so, despite being asked directly, over and over again.

An early, tenacious critic was Karl Popper whose 1934 book Logik der Forschung, arriving in English in 1959 as The Logic of Scientific Discovery, directly answered verificationism. Popper heeded the problem of induction as rendering empirical verification logically impossible.[38] And the deductive fallacy of affirming the consequent reveals any phenomenon's capacity to host over one logically possible explanation. Accepting scientific method as hypotheticodeduction, whose inference form is denying the consequent, Popper finds scientific method unable to proceed without falsifiable predictions. Popper thus identifies falsifiability to demarcate not meaningful from meaningless but simply scientific from unscientific—a label not in itself unfavorable.

Popper finds virtue in metaphysics, required to develop new scientific theories. And an unfalsifiable—thus unscientific, perhaps metaphysical—concept in one era can later, through evolving knowledge or technology, become falsifiable, thus scientific. Popper also found science's quest for truth to rest on values. Popper disparages the pseudoscientific, which occurs when an unscientific theory is proclaimed true and coupled with seemingly scientific method by "testing" the unfalsifiable theory—whose predictions are confirmed by necessity—or when a scientific theory's falsifiable predictions are strongly falsified but the theory is persistently protected by "immunizing stratagems", such as the appendage of ad hoc clauses saving the theory or the recourse to increasingly speculative hypotheses shielding the theory.

[…]Popper developed the general epistemology critical rationalism, which finds human knowledge to evolve by conjectures and refutations. Popper thus acknowledged the value of the positivist movement, driving evolution of human understanding, but claimed that he had "killed positivism”.

Joe: With science one needs a way to test the claims made. With evolutionism there isn't any way to test its claims.

From http://ncse.com/cej/6/2/what-did-karl-popper-really-say-evolution What Did Karl Popper Really Say About Evolution?

The fact that the theory of natural selection is difficult to test has led some people, anti-Darwinists and even some great Darwinists, to claim that it is a tautology. . . . I mention this problem because I too belong among the culprits. Influenced by what these authorities say, I have in the past described the theory as "almost tautological," and I have tried to explain how the theory of natural selection could be untestable (as is a tautology) and yet of great scientific interest. My solution was that the doctrine of natural selection is a most successful metaphysical research programme. . . . [Popper, 1978, p. 344]

I have changed my mind about the testability and logical status of the theory of natural selection; and I am glad to have an opportunity to make a recantation. . . . [p. 345]

The theory of natural selection may be so formulated that it is far from tautological. In this case it is not only testable, but it turns out to be not strictly universally true. There seem to be exceptions, as with so many biological theories; and considering the random character of the variations on which natural selection operates, the occurrence of exceptions is not surprising. [p. 346]

from the article itself..

What Popper calls the historical sciences do not make predictions about long past unique events (postdictions), which obviously would not be testable. (Several recent authors—including Stephen Jay Gould in Discover, July 1982—make this mistake.) These sciences make hypotheses involving past events which must predict (that is, have logical consequences) for the present state of the system in question. Here the testing procedure takes for granted the general laws and theories and is testing the specific conditions (or initial conditions, as Popper usually calls them) that held for the system.

A scientist, on the basis of much comparative anatomy and physiology, might hypothesize that, in the distant past, mammals evolved from reptiles. This would have testable consequences for the present state of the system (earth's surface with the geological strata in it and the animal and plant species living on it) in the form of reptile-mammal transition fossils that should exist, in addition to other necessary features of the DNA, developmental systems, and so forth, of the present-day reptiles and mammals.

The reasoning is in the comment I wrote. The quotes are references, as many simply ignore them, do not understand the context and/or flat out misrepresent them.

To use you as an example from a previous thread...

eklektos: People who work in the field agree that life requires a F,G, or mid K main sequence star. The list of habitability factors last I heard was a minimum of 26. It's probably gone up as they keep finding more. See spectral class:

[actual quote from spectral class section, which is mostly concerned with requirements for life to evolve]

Scott: [so] it seems you didn’t actually understand the article you referenced, as the “people who actually work in the field” you appealed to in the Spectral Class section are mostly referring to factors favorable for life to evolve, not for preexisting life to survive.

Yet, you do not think life evolved in the first place. So, apparently, you don’t even take your own arguments seriously.

1. The arch is an example of human design, is Landscape Arch is an arch.

2. How can test the claim that it can only be designed? If not then there is nothing to refute.

3. ToE requires that the closer related the more similar because of the mechanism posited , ID by definition can say nothing about how or why something is designed. It cannot speak to any aspect of design choice without some knowledge of the designer.

Evolutionism posits a somewhat gradual, incremental evolution driven by culled genetic accidents. Natural selection, a process of elimination, is said to be blind, mindless and incorporates heritable random, as in happenstance/ accidental, mutations. Dawkins calls it blind watchmaker evolution.

What we need is a way to model what mutations do. That is something beyond the piddly changes we observe. Changes in beak size does not explain the finch. Anti-biotic resistance does not explain bacteria. Moth coloration does not explain the moth. Changes in eye color does not explain the vision system nor the type of eye nor the organism. An albino dwarf with sickle-celled anemia is what we can get when mutations accumulate. Not quite what evolutionism requires.

We need to be able to test the hypothesis that changes to genomes can account for the diversity of life starting from the first populations as Darwin saw it- simple prokaryotes. Only then could we determine if natural selection is up to the task. But thanks to the current state of biology being dominated by blind watchmaker evolution, no one has any idea what makes an organism what it is and the evidence is against the “organisms are the sum of their genome"

Joe: OK how can we test the claim that natural selection is a designer mimic [or that] natural selection produced any bacterial flagellum?

See my comment below. We conjecture theories about how the world works, in reality, that would have necessary consequences for the current state of the system. This is something we can actually test in the present.

Testing a theory means we take it seriously, as if it was true in reality - along with the rest of our current, best theories, as if they were also true in reality.

All of these theories, considered concurrently, would have necessary consequences for the current state of the system, which we can test. Criticism has scientific character when it takes the form of empirical observations, which should conform to the necessary consequences.

To apply this in the case of natural selection as a design mimic, we would determine what the necessary consequences were for both biological darwinism, which includes natural selection, and an abstract designer with no defined limitations. The problem is, there would be no necessary consequences for an abstract designer. It’s unfalsifiable. On the other hand, there would be necessary consequences for biological darwinism. I’ve outlined them in a related comment below.

Again, before you right this off as a “philosophical rant”, I’d point out that irreducible complexity is based on the underlying explanation that specific biological features could have been built if the knowledge of how to build them had already existed, rather than having genuinely been created.

Again, my comment below addresses how this is relevant to finding a rabbit in the precambrian as well.

What basic structure. It's not a monotreme or a therian. It's a eutriconodont. And once again to quote Nature:

The evolutionary relationships of the fossil suggest that either the ‘modern’ middle ear evolved twice, independently or that it evolved and was then lost in at least one ancient lineage.

And nobody puts it in a straight line lineage to the DMME. Further there may be some functional advantage for having the mandible attached to the inner ear. But as it's a fossil we have no way of knowing. Plus reasoning from morphology is circular, particularly when you don't have live specimens, or even tissue to evaluate. Liaoconodon hui and Yanocodon are both too late to be transitional anythings.

The connected ear and jaw structure is similar to the embryonic pattern in modern monotremes (egg-laying mammals) and placental mammals, but is a paedomorphic feature retained in the adult, unlike in monotreme and placental adults. This suggests that reversal to (or retention of) this premammalian ancestral condition is correlated with different developmental timing (heterochrony) in eutriconodonts

Let me address this whole silly ape thing. Humans and apes are "similar" in superficial ways. Apes have different pelvis' and feet from humans. Different leg bones. These are the very upstream networks I was discussing. If you give an ape a human foot it's at a disadvantage. why? It will not be able to climb efficiently, and without the human pelvis and legs it will not be able to walk efficiently. So it will be someone's lunch. Afarensis was a knuckle walking ape. It did not have a human pelvis and to date there has been no foot found for afarensis, so we don't even know what it's foot looked like. They have claimed that an isolated metatarsal found in a conglomeration of bones belonged to afarensis. However there is absolutley no proof of that. It looks exactly like a human metatarsal. It was not found with an afarensis skeleton but in a jumble of bones. The study of these bones found in hadar formation stated We assign AL 333-160 [the bone’s designation] to A. afarensis, the only hominin species in an assemblage of [more than] 370 hominin specimens so far recovered from the Hadar Formation.” Why? Because they assumed humans didn't live during this time, not on any objective evidence. Another just so story. A human foot without the rest of the skeletal architecture to support it would put the animal at a competitive disadvantage and would be selected out.

Nic: As such, you're demands that CH rigorously define his view of science rings totally hollow when you refuse to define yours.

Again, CH is the one making the claim that evolutionary theory is not "science", not me. As such, it is CH that needs to define what he means by "science".

If, by "science" Cornelius means logical positivism, then so what? We discarded LP because it did not withstand criticism. If, by "science", Cornelius means empiricism, again, so what? We have made progress since then as well, and have many good criticisms of it which have gone unaddressed. Many of which I have referenced here, which include the role of empirical observations, the relevance of probability in adopting theories, etc.

All of these issues are key assumptions in his arguments, yet he has yet to clearly define or argue for them in any sort of rigorous way.

Furthermore, I have presented arguments for a particular philosophy of science: Karl Popper's critical rationalism. And I've argued how evolutionary theory is scientific under CR, in detail.

So, I've been more that forthcoming, despite the burden of defining science being on Cornelius, not me.

It's not. Biology is a science, but biology is not evolution and evolution is not biology.

Trivially true but irrelevant since no one is claiming that biology and evolution are the same thing.

Science, in part, is a process of methodical investigation of the observable and inferable world. It involves the collection of data through observation by various means, not just unaided human senses, and the construction of provisional explanations that try to account for it. An unorganized collection of raw data is of little use on its own but, when arranged according to a theory of how it is all related, it can offer profound insights into how the natural world works. This is why a well-substantiated and fruitful theory is the most highly-prized product of any science. Whatever its alleged and actual shortcomings, evolution is such a theory in biology.

You and other evolutionists are confusing a philosophy of scientific interpretation with the discipline of science itself. So in your world only 'evolutionary science' qualifies as actual science.

No, doing science qualifies as science. If ID proponentsists want their ideas to be taken seriously as science then they must actually do some science, which is a lot more than just trying to pick holes in a theory they dislike for religious as much as scientific reasons.

Nothing could be further from the truth, and until you and others learn that fact you will continue to be frustrated in your attempts to understand alternate views as you completely fail to face the fact that such alternate views exist and are legitimate.

Science couldn't care less about whether alternate views are "legitimate", whatever that might mean. What concerns it is which - if any - of them have any explanatory power or basis in fact.

"Trivially true but irrelevant since no one is claiming that biology and evolution are the same thing."

Perhaps you're not, but it's palpable nonsense to claim no one does.

"Whatever its alleged and actual shortcomings, evolution is such a theory in biology."

Only if you accept the use of rubber rulers. Similarity is proof of evolution, but so is uniqueness. Traits are inherited from a common ancestor, but they also result from convergence. Regardless of the evidence it is made to fit the paradigm of evolution.

"No, doing science qualifies as science. If ID proponentsists want their ideas to be taken seriously as science then they must actually do some science, which is a lot more than just trying to pick holes in a theory they dislike for religious as much as scientific reasons."

Perhaps if you would actually spend some time doing a little reading you would come to see this argument is easily refuted. As for evolution, just how does it do science? It simply takes scientific research and spins it through the evolutionary filter. That traits are inherited is a fact, that they come about by evolutionary mechanisms is nothing but an interpretation.

"Science couldn't care less about whether alternate views are "legitimate",..."

One hopes that in time you will come to understand the utter foolishness of this statement.

nic: Perhaps you're not, but it's palpable nonsense to claim no one does.

Evolution is the central unifying theory of biology. They're not the same thing, though.

nic: Regardless of the evidence it is made to fit the paradigm of evolution.

Lots of evidence could contradict evolution; there just no such evidence.

nic: Perhaps if you would actually spend some time doing a little reading you would come to see this argument is easily refuted.

We read a lot. There's virtually no science done by IDists, though they do publish sciency stuff.

nic: As for evolution, just how does it do science?

This month, Nature has a nice study on the rapid evolution of influenza, and another on using phylogenetics to trace the source of infections. Science has a study of poop, and the evolution of intestinal viruses. Paleontology shows off a new specimen of Yunguisaurus.

"Lots of evidence could contradict evolution; there just no such evidence."

There is no evidence which allowed to contradict evolution. Regardless of what is found it is made to fit. Evolution has made man altruistic, except when it made him selfish. Similarity is the result of common descent except when it's not common descent but convergence.

So yes, there is lots of evidence which contradicts evolution, it simply has a rubber ruler applied to it.

"There's virtually no science done by IDists, though they do publish sciency stuff."

Nonsense. Any one possessing a Phd has done plenty of science or they would not posses the degree. This is nothing more than another asinine statement of the type all too common among evos

"This month, Nature has a nice study on the rapid evolution of influenza,..."

This is work based on biology and as biology is not dependent on evolution, and as evolution is nothing more than a philosophy used to interpret results, you might want to try again to answer how evolution does science. This response does not even come close.

nic: Evolution has made man altruistic, except when it made him selfish.

They're called countervailing influences. Any theory should explain the facts, and it turns out that people are selfish and altruistic.

nic: Similarity is the result of common descent except when it's not common descent but convergence.

Common descent is supported by the pervasive nested hierarchy. Convergence supports natural selection. See Darwin 1859.

nic: Any one possessing a Phd has done plenty of science or they would not posses the degree.

A PhD in science implies having done some science.

nic: This is work based on biology and as biology is not dependent on evolution,

Um, it was based on evolutionary theory.

Łuksza & Lässig, A predictive fitness model for influenza, Nature 2014: "The seasonal human influenza A/H3N2 virus undergoes rapid evolution, which produces significant year-to-year sequence turnover in the population of circulating strains... From fitness and frequency of each strain, we predict the frequency of its descendent strains in the following year."

You're really going to use the nested hierarchy canard? As for convergence, you must first provide proof the similarities are the result of convergence. You can't. As for Darwin, perhaps you could point me to a scientist.

"Um, it was based on evolutionary theory."

So? Do you suppose the results would be different if the work was done by a creationist biologist?

"The seasonal human influenza A/H3N2 virus undergoes rapid evolution, which produces significant year-to-year sequence turnover in the population of circulating strains... From fitness and frequency of each strain, we predict the frequency of its descendent strains in the following year."

Joe: With science one needs a way to test the claims made. With evolutionism there isn't any way to test its claims.

Again…

Knowledge, as I’m about to use it, is useful information that tends to remain when embedded in a storage medium. It plays a causal role in it’s preservation in that medium. This includes books, brains and even genomes. We put good ideas in books, and keep them there, because they are good ideas. They allow us to make progress. So, good ideas play a causal role in their preservation.

Biological Darwinism is the theory that the knowledge of how to build concrete biological adaptations was genuinely created (not having existed before in some other form) via a form of conjecture and refutation. Specifically, conjecture, in the form of genetic variation, and refutation, in the form of natural selection. Biological Darwinism falls under the umbrella of our current, best explanation for the universal growth of knowledge. In the case of genomes, knowledge represents the instructions of what transformations will result in concrete biological adaptations.

As indicated in the referenced NCSE article, the historical sciences do not make predictions about long past events, as that would be untestable, which is apparently what Joe is referring to. Rather, we conjecture explanations about how the world works, in reality, which must have logical consequences for the present state of the system in question, which is testable. This includes the idea that biological complexity emerges from variation and selection.

Good theories prohibit things, and biological darwinism is no exception. If the knowledge of how to build concrete biological adaptations was genuinely created by variation and selection (trial and error in the form of non-explanatory knowledge), that would have logical consequences for the present state of the system in question, which is testable. Just one such example, is that we should see organisms appearing in the order of least to most complex. We should not see organisms appearing all at once. Nor should we see them appear in the order of most complex to least complex. Nature cannot build organisms until the knowledge of how to build them has been created.

On the other hand God supposedly knows everything logically possible. As such he would posses the knowledge of how to build any organism that has existed, does exist or could possibility exist. In the same sense, ID’s designer is conveniently abstract and has no defined limitations. This includes lacking the limitation of not knowing how to build any organism that has, does or could exist. As such, there is no such corresponding necessary consequence of God or ID’s designer in the current state of the system. Both would be free to create organisms all at once, or in any order, including most complex to least complex. It’s unfalsifiable.

Furthermore, I have yet to hear any sort of valid criticism to this argument. At best, it’s claimed to be a “philosophical rant”.

However, I’d point out this is the underlying explanation for why finding a rabbit in the Precambrian would falsify biological darwinism, as it would imply that the knowledge of how to build rabbits was created in some other way. This represents a definition of science that is not merely prophecy, but an explanation about how the world works, in reality. Nature couldn’t build a rabbit until the knowledge of how to build them had been created.

I’d also point out that an observation of finding a rabbit in the Precambrian is itself theory laden since it is based on the theory that different layers of strata were laid down in chronological time. Should we actually find a rabbit in the Precambrian there is always the possibility that the observation is in error rather than the theory itself. As such, we would look for a better explanation for how that rabbit got there before falsifying biological Darwinism. For example, it could have been planted there. Or there could be due to a previously known or unknown exception for how strata is laid down. As such, we would conjecture explanations for why the rabbit would appear there and criticism them. “That’s just what God/ID’s designer must have wanted” is a bad explanation for reasons I've explained elsewhere. (It's easily varied)

Again, before you classify this merely as a “philosophical rant”, I’ve given a concrete example of this with the 2011 OPRA experiment regarding neutrinos in a comment above. We did not immediacy falsify GR, because we lacked a good explanation as to why neutrinos traveled faster in just the OPERA experiment. Rather, we conjectured theories about why the observation was wrong and found them.

Let me address this whole "parsimony" nonsense. No afarensis skeleton has been found with feet. So the most parsimonious explanation is that afarensis had no feet. Babbling about parsimony is simple minded, which is very parsimonious.

You wasted a lot of verbiage saying what I could have said in two words. straw man. Now I burned the little booger to make a point. All things are not equal. There has been no afarensis skeleton found with feet. There has been a human metatarsal found in the Hadar formation. So the most parsimonious explanation is there were humans around during the same time as afarensis. Again, to quote from the statement of classification:

“We assign AL 333-160 [the bone’s designation] to A. afarensis, the only hominin species in an assemblage of [more than] 370 hominin specimens so far recovered from the Hadar Formation.”

There's you're reference, remember it. When I talk about afarensis foot you'll know. This classification was done solely on the basis of Darwinian assumptions, not on parsimony. Hennigian cladistics assumes Darwinian evolution. How I choose to classify organisms depends on my goal. Hennigian cladistics goal is to classify organisms according to Darwinian principles. Therefore it cannot be used to prove Darwinian evolution.

Ok, lets the idea that afarensis lacked feed seriously, in that it’s true in reality, along with all of our current, best explanations, and that all observations should conform to them.

How did they avoid predators? How did they forage for food? How did they migrate, given the rest of the bones we have found? How did any of them grow into adult hood, so we could eventually find a fossilized version of an adult afarensis?

IOW, when we take into account the rest of our best explanations for how organisms compete and survive, the idea that afarensis lacked feet does not survive criticism.

eklektos: There has been a human metatarsal found in the Hadar formation... “We assign AL 333-160 [the bone’s designation] to A. afarensis, the only hominin species in an assemblage of [more than] 370 hominin specimens so far recovered from the Hadar Formation.”

So the formation contains 370 A. afarensis, and no modern humans. Indeed, nowhere in the world have modern humans been found in such old strata. But you want to assign the foot to a modern human. That makes no sense, of course. In any case, you don't need the foot to determine gait, which can be determined by the hip and the spine.

So the formation contains 370 A. afarensis, and no modern humans. Indeed, nowhere in the world have modern humans been found in such old strata.

Well there is al-666-1 a Homo Habilis jawbone in the hadar formation

http://www.ncbi.nlm.nih.gov/pubmed/9209580

And of course Kadanuumuu which has been assigned a designation of afarensis, despite having no skull and features that are distinctly different from Afarensis. Such as long bones like genus homo. Barrel chest like genus homo. Notice that the skeleton in not in the range of afarensis but within the range of Homo. It's shoulder blade is like that of a modern human. So it must be an australopithicine!

http://www.ncbi.nlm.nih.gov/pubmed/23097193

But you want to assign the foot to a modern human. That makes no sense, of course.

So yea, pretty much. Makes perfect sense when you look at the evidence. But of course Darwinist can't have that! And they're honest seekers for the truth! There's a saying in the south. "Don't urinate down my back and tell me it's raining."

In any case, you don't need the foot to determine gait, which can be determined by the hip and the spine.

Well, except that the spine is not homo and wouldn't support the weight of bipedal walking for long periods of time. And that the hip is purely a figment of Darwinists imagination. Lucy's hip is at the wrong angle, and she has a conical chest which wouldn't support bipedal arm swing. And Sideba is missing the portions of the hip that would allow us to judge it's gait. Then there's are swing. Selam has a apes shoulder blade, so lets chose Kadanuumuu because he suits our purpose. Viola! Johnny Cash's Cadillac.

Nic: Nothing could be further from the truth, and until you and others learn that fact you will continue to be frustrated in your attempts to understand alternate views as you completely fail to face the fact that such alternate views exist and are legitimate.

The existence of alternate views of “science” is precisely my point. And they are defined rigorously in the philosophy of science. It’s unclear why this is so difficult for you to understand, given that you just appealed to diversity above, although rather poorly.

Specifically, not all views of science are legitimate or even relevant to the issue at hand because we’ve discarded them. Yet Cornelius keeps claiming evolution isn’t science without disclosing which view he actually holds or arguing for it’s legitimacy. In fact, he even changes his view mid argument, as I’ve illustrated above, whenever it happens to suit his purpose.

Furtermore, AFAIK, he hasn’t even acknowledged the issue, despite having brought it up explicitly, over and over again. At best, we get people, such as yourself, that do not understand how this undermines his argument, yet try to defend him.

Again, why does Cornelius need people to speak for him? Can’t he answer questions on his own? What else are we supposed to conclude from his silence on this issue?

Scott: What else are we supposed to conclude from his silence on this issue?

Velikovskys: Only that he chooses not to respond. Why is purely speculative.

Are you suggesting we cannot conjecture and criticize ideas about why Cornelius is silent to make progress. All ideas *start out* as speculation. What sets them apart as knowledge is criticism. Why is Cornelius' silence any different? His objections do not exist in a vacuum.

Why would he not even acknowledge the issue. At all. Period? He could easily put the issue to rest, once and for all, yet he has not.

For example, is Cornelius limited by the number of characters in a blog post? No, he's not. Even if that was the case, he could start an entire post about just that issue. Does he not have enough time? Again, he could simply put off writing some other blog post to make time. We can say the same about having enough bandwidth, blogger limiting the number of posts, etc.

Is he ignorant about the philosophy of science? This seems unlikely because he has quote mined passages from books on the philosophy of science. Not to mention that I’ve posted numerous links, quotes and references to difference philosophies of science, in detail. Furthermore, this was likely part of his college curriculum.

Would disclosing his definition expose his argument to additional criticism? Yes, it would. Furthermore, he knows his target audience already shares the same conception of human knowledge. As such, he doesn’t need to convince them of something they already believe, so hy exposes himself to more criticism? It simply doesn’t suit his purpose.

What else are we supposed to conclude? Does anyone have a better explanation? I’m asking for criticism. That’s how we make progress.

Cornelius thinks we cannot make progress unless he explicitly discloses his position. But that’s no different that assuming we cannot make progress on evolutionary theory without explicitly observing humans evolve from a common ancestor we share with great apes.

Scott: Scott:Again, why does Cornelius need people to speak for him? Can’t he answer questions on his own? What else are we supposed to conclude from his silence on this issue?

J: That he knows a brick wall when he sees one. His posts are written to those who use standard inductive criteria. All that is relevant to the fraud called "evolutionary science" is your own admission that most of such scientists believe in positive evidence which you rightly deny exists for the hypothesis of UCA.

wait, Scott, are you allowing us to use inductive reasoning again? Please say no, because scrolling by everything you say has been saving me a LOT of time. Wait a minute... maybe it has been saving Cornelius a lot of time!!!

velikovskys: Only that he chooses not to respond. Why is purely speculative.

While we're speculating, it could because Cornelius Hunter is in awe of the power of Scott's argument. Or not.

While we can't know Cornelius Hunter's reasons with any certainty, we can certainly criticize the hole in his argument. If he claims that evolution is not science, and we don't know what he means by science, then his claim is not well-defined. We don't necessarily have to have a precise definition of science, but at least a general idea would be helpful.

You’re being vague, Jeff. Are you saying Cornelius is silent because he can identify architectural structures? That simply doesn’t follow. Perhaps you’re implying something else?

Jeff: His posts are written to those who use standard inductive criteria.

Cornelius is silent because his posts are written to people who use a vague standard that you haven’t defined? Why would that prevent him from even acknowledging the question? This simply doesn’t follow either. There is standard far more rigorous that your vague “inductive criteria”, called Logical Positivism, yet we’ve discarded it because it did not withstand criticism. If no one actually uses this “inductive criteria” then why should we care? Your refusal to define it in a rigorous way doesn’t help, either.

Jeff: is your own admission that most of such scientists believe in positive evidence which you rightly deny exists for the hypothesis of UCA.

First, you are quibbling over definitions. Evidence that strongly collaborates a theory could be described as positive evidence. This isn’t necessarily the same thing as thinking evidence positivity proves anything is true in the epistemological sense.

Second, even if they did, I’ve already made the distinction that disagreeing on the role that empirical evidence plays is not the same a disagreeing if there is relevant empirical evidence at all. Your continual refusal to acknowledge this distinction, despite having made it over and over again, is an example of a refusal to rigorously define science.

Scott: are you suggesting we cannot conjecture and criticize ideas about why Cornelius is silent to make progress

velikovskys: That is what I just did.

Yet, we’e ruled out there being a Blogger specific technical issue that prevents him from doing so. We’ve also ruled out Cornelius not having time to post about it, as he could have written this post about the issue instead, should he have chosen to do so.

Furthermore, we’ve ruled out that he is completely ignorant that other definitions of science exist, or that there would be no implications of him actually doing so.

I’ve also criticized the conjectured ideas that Jeff just presented. They are vague. We’ve make progress on this front as well.

Scott: All ideas *start out* as speculation. What sets them apart as knowledge is criticism

velikovskys: I always thought it was additional data.

Additional data indicates where there are problems, not the solutions to those problems. It does not fill in the gap implied by the data. In many cases, the data is in conflict with other data, which means at least one of our theories is in error. iIt’s unclear how data we’ve found to be in conflict can be an explanation of how to solve the same problem. It’s a category error.

Scott; Why is Cornelius' silence any different? His objections do not exist in a vacuum.

velikovskys: No speculate away. But at this point we only know that he is silent.

So, if Cornelius told us why he was silent, we wouldn’t have to speculate? How would we know he was telling the truth. Even if he was being truthful about his experience, he could be confused or mistaken about the explanation behind his actions.

zachriel:While we can't know Cornelius Hunter's reasons with any certainty, we can certainly criticize the hole in his argument.

Of course, I have myself.

If he claims that evolution is not science, and we don't know what he means by science, then his claim is not well-defined.

That is logic not speculation.

We don't necessarily have to have a precise definition of science, but at least a general idea would be helpful.

Not to his case it wouldn't.

But that is beside the point, "What else are we supposed to conclude from his silence on this issue?

It could be

1 it could because Cornelius Hunter is in awe of the power of Scott's argument. 2 That he knows a brick wall when he sees one. His posts are written to those who use standard inductive criteria. 3 Please say no, because scrolling by everything you say has been saving me a LOT of time. Wait a minute... maybe it has been saving Cornelius a lot of time!!! 4 he believes in the proverb Even a fool, when he holdeth his peace, is counted wise: and he that shutteth his lips is esteemed a man of understanding.

Zachriel: We don't necessarily have to have a precise definition of science, but at least a general idea would be helpful.

A general idea that lacks a coherent definition of the role of empirical evidence in science, or how it is applicable in the formation and adoption of theories isn't very helpful. Nor does it lend itself to criticism.

For example, in this post alone, Cornelius' position on the role observations play in science were all over the map. In the absence of such a definition, he is merely simply slinging mud at a theory he personally finds objectionable in hope that something sticks.

Furthermore, it's not a unreasonable burden because there are well defined philosophies of science that he can reference.

I'm not asking for an essay. I'm asking for his views on key issues are relevant to the claim he made in the first place.

Scott: There is standard far more rigorous that your vague “inductive criteria”, called Logical Positivism, yet we’ve discarded it because it did not withstand criticism.

J: How is logical positivism more rigourous than the inductive criteria of parsimony and breadth of predictive explanation? Positivism is self-evidently non-sense.

Scott: If no one actually uses this “inductive criteria” then why should we care?

J: I hear of the criteria of parsimony of breadth of predictive explanation being applied to hypothesis rejection all the time.

Scott: Your refusal to define it in a rigorous way doesn’t help, either.

J: What's hard about the concept of parsimony applied to the number of axioms required to predict? What's hard about the breadth of predictive explanation to understand?

Scott: First, you are quibbling over definitions. Evidence that strongly collaborates a theory could be described as positive evidence.

J: But that's because the very meaning of "corroborate" (which I assume you meant) is what plays into the parsimonious and breadth of an explanation--IOW, inductive criteria. And those criteria are the criteria for positive evidence, at least in the sense of warranted belief. A belief/inference can be dead wrong and still be warranted in that sense.

Scott: This isn’t necessarily the same thing as thinking evidence positivity proves anything is true in the epistemological sense.

J: Of course not. That's why we have to distinguish between warranted belief and TRUE warranted belief to make sense of positive evidence. A predictive explanation that best satisfies the inductive criteria can be false AND warranted. The latter is what we mean by "evidentially-supported."

Scott: Second, even if they did, I’ve already made the distinction that disagreeing on the role that empirical evidence plays is not the same a disagreeing if there is relevant empirical evidence at all.

J: It's only different in the minimal sense. THAT there is stuff "out there" is an inductive inference. And how would you go about showing that metaphysically phenomenalist theory is more parsimonious or has greater predictive breadth than the view that there's stuff "out there" that mediates "information" to us via other stuff "out there?" If you can show this, I'll become a metaphysical phenomenalist. I don't know how to do it.

In the meanwhile, the most parsimonious explanation of the coincidence of two-dimensional visual data and seeming locations of sensations of touch/feel seems to be that there are extended entities or composites of rapidly moving extended entities "out there."

J: Evolution per se is as science as you can get. But UCA is an historical belief. There are no axioms written down anywhere that imply any particular UCA tree including fossil and extant species occurred in earth history. Thus, there are no tests of those non-existent axioms. Thus, the belief in UCA is a non-scientific belief. Inductive criteria apply to explanations, not beliefs per se.

Agreed. Something would be better than nothing, as it would be a starting point for criticism.

But that’s the problem. Implicit in presenting such an outline would be the concession that his argument assumes a particular philosophy of science. It would open up a whole can of worms, which he would have to argue for and expose him to additional criticism. This simply doesn’t suit his purpose.

However, this does not prevent Cornelius from making such an appeal when it does suit his purpose, such as attacking the NSF Science and Engineering Indicators report.

That is because neither statement makes sense. In order to make a meaningful statement about what goes around what, one first needs to specify a frame of reference. For an observer on the sun, the Earth circles the sun. And for an observer on Earth, the sun circles the Earth. That is “factual knowledge.”

I’m simply pointing out that, in order to make a meaningful objection that Evolutionary theory is not a scientific theory or scientific fact, he needs to specify what he means by science, including actually defining the term scientific fact, etc.

Furthermore, the above claim that “neither statement makes sense” depends on a very specific assumption about science. Namely, that science is about what people will experience, rather than explanations about how the world works, in reality. (At which point science stops being about anything but one’s own experiences) I’d note that In the case of the latter the question does make sense and the correct answer is “the sun goes around the earth”.

So, it’s not as if Cornelius is oblivious to the issue. Furthermore, Nor am I merely being pedantic as I’ve illustrated how it is highly relevant to the arguments he presents.

It's not. Biology is a science, but biology is not evolution and evolution is not biology. Genetics is a science, but genetics is not evolution and evolution is not genetics. You and other evolutionists are confusing a philosophy of scientific interpretation with the discipline of science itself. So in your world only 'evolutionary science' qualifies as actual science.

Nothing could be further from the truth, and until you and others learn that fact you will continue to be frustrated in your attempts to understand alternate views as you completely fail to face the fact that such alternate views exist and are legitimate.

As such, your demands that CH rigorously define his view of science rings totally hollow when you refuse to define yours.

No, because it's simply a logical fact. Biological systems and genetic codes existed before the concept of evolution and will exist after the demise of evolution, so obviously neither discipline is a de facto part of evolution or dependent on evolutionary thought. They stand on their own completely removed from evolutionary dogma. If you cannot understand that plain fact I doubt you will ever come to understand or appreciate a viewpoint other than the very narrow outlook you now posses.

"Why don't you start out by explaining how science works, in detail, then point out how biological Darwinism doesn't fit that explanation. Please be specific."

You're a real piece of work. You always demand everyone provide detailed and specific explanations while you continuously toss around vague generalities. Obviously such forums as these are not the venue for the detail you demand.

As for science, it is quite simply a discipline of study which depends on a system of repeatable, observable, demonstrable and testable actions. Evolution can perform none of these. It is nothing more than a philosophical viewpoint which calls upon scientific disciplines in an attempt to justify its world view.

"Any takers?"

How about you? Let's hear from you in extreme detail and specificity how evolution meets the basic demands of scientific enquiry.

You could start with details and specifics of observable evolution. You could follow that up with specific and detailed examples of repeated evolution and examples of demonstrated evolution. How about repeatable, demonstrable and observable examples of the origin of life?

No one will be holding their breath.

"It’s unclear why this is so difficult for you to understand, given that you just appealed to diversity above, although rather poorly."

I understand it all to well, and because you can't follow a simple argument is no reason to question my ability to express a point. However, such attitudes are all too typical of evos.

"Specifically, not all views of science are legitimate or even relevant to the issue at hand because we’ve discarded them."

Which views would those be and who determined they should be discarded?

Nic: Biological systems and genetic codes existed before the concept of evolution and will exist after the demise of evolution, so obviously neither discipline is a de facto part of evolution or dependent on evolutionary thought.

Physics existed before the field of physics exited. Yet, that doesn’t make the field of physics irrelevant. So, apparently, you’re singling out evolutionary theory for some other reason than they are not equivalents, which is undisputed. This is simply hand waving.

Again, Cornelius is the one claiming evolution isn’t science. As such it’s his burden to define what he means by science. Otherwise, it might as well claim that evolutionary theory is not “mufados”, “hiponix” or some other meaningless word. If you can’t see this is his burden, it’s unclear how further discussion will be fruitful.

Nic: As for science, it is quite simply a discipline of study which depends on a system of repeatable, observable, demonstrable and testable actions.

And I’m being vague? Take any philosophy of science and compare to what you just wrote. You’ll find none of them fit what you just described because it’s highly ambiguous. Rigorous definitions exist. They can be referenced by name and criticized. Caveats can be indicated. Or Cornelius could simply say he disagrees with all philosophies of science. Yet, none of these things have occurred.

Nic: How about you? Let's hear from you in extreme detail and specificity how evolution meets the basic demands of scientific enquiry.

First, It’s not my burden. I’m not the one making the claim.

Second, despite being under no obligation to do so, I already have. I’ve posted several references in this thread alone, among dozens of others. (Here’s a hint: look up Karl Popper’s Critical Rationalism).

Nic: You could start with details and specifics of observable evolution. You could follow that up with specific and detailed examples of repeated evolution and examples of demonstrated evolution. How about repeatable, demonstrable and observable examples of the origin of life?

This is why it’s important to define what science is. Or, more importantly, what it is not. Science isn’t about stuff you can observe, because all observations are theory laden. This includes things right in front of you. Of course, feel free to explain how it’s possible to extrapolate observations without first putting them into an explanatory framework. You’ll be famous.

Observations are plentiful, what is scarce is good explanations for those observations, which are assertions about how the world works, in reality.

To use an example, when you look at a sample in a microscope, you’re not looking at it directly. What you’ve done is introduce equipment that will relay accurate information about the sample according to your explanation of how the equipment works.

As I mentioned earlier, good theories prohibit things. We accept observations from microscopes, or any other equipment, because we have good explanations about how they work, which constrains what parts they require and how they must be configured to actually give you accurate information about the sample. For example, you can’t put a roll of quarters into a microscope, instead of a lens, and expect to see bacteria. So, being able to set up equipment properly to get evidence depends on having a good explanation of how it works. Eyes are, effectively, equipment. When they are configured incorrectly, due to macular degradation or some other biological issue, we do not expect to see the external world clearly. The same can be said about the the optic nerve, our brain, etc.

So an observation is always an explanation, regardless if it’s sitting right in front of you, or halfway across the galaxy. The explanation always comes first, not vice versa. Empiricism represented progress because it promoted the value of empirical observations. However it was mistaken in that it got the role of empirical observations backwards.

When we turn the role of empiricism on it’s head, your demands become unreasonable and even undesirable. This is why it’s important for CH to define what he means by science.

Nor am I simply pulling this out of my *ss. Again, go look up Popper’s Critical Rationalism. It’s well defined. It flips the role of empirical observations on its head. Read Popper’s books, the Logic of Scientific Discovery, Objective Knowledge, etc.

Also, see the NCSE article I quoted above, which explains how biological Darwinism *is* falsifiable.

Nic: Which views would those be and who determined they should be discarded?

Are you saying that specific philosophies of science, such as Logical Positivism, have not been discarded due to criticism? Is that what you’re really trying to imply?

"Physics existed before the field of physics exited. Yet, that doesn’t make the field of physics irrelevant. So, apparently, you’re singling out evolutionary theory for some other reason than they are not equivalents, which is undisputed. This is simply hand waving."

If this wasn't so pathetic it would actually be funny. Anyway, when did I ever say, or even imply that biology or genetics were irrelevant? This demonstrates poor reading comprehension, or a deliberate attempt to misrepresent what I said. Perhaps it's both. Nevertheless it's very pathetic.

" As such it’s his burden to define what he means by science."

That's simply typical of the poor logic I have come to expect from evos. You're making a claim to a definition of science and as such you have a burden to define your position as well. I expect your problem is you don't sufficiently understand the subject.

As for evolution being science, I would appreciate you demonstrating exactly how evolution qualifies as science on its own merits.

"You’ll find none of them fit what you just described because it’s highly ambiguous."

I must disagree, my statement is perfectly clear. Of course when someone as confused as you reads a simple statement I'm not surprised it seems ambiguous.

"It’s not my burden. I’m not the one making the claim."

But you most definitely are the one making the claim.

"Science isn’t about stuff you can observe, because all observations are theory laden."

That's just plain funny. That's all I can say about that.

"without first putting them into an explanatory framework,..."

That's your favourite line, why not put that theory into an explanatory framework for those of us not quite as smart as you.

"To use an example, when you look at a sample in a microscope, you’re not looking at it directly."

So because I wear glasses I never look at anything directly? You just keep coming up with one zinger after another. You took a whole paragraph to say absolutely nothing, are you aware of that?

"Are you saying that specific philosophies of science, such as Logical Positivism, have not been discarded due to criticism? Is that what you’re really trying to imply?"

You don't read well, do you? I asked simple question which you failed to answer, again.

Gee whiz. Try to use a consistent definition of body plan, or bauplan. IDers constantly claim that there have been no new body plans since the Cambrian Explosion

Two arms, two legs, a torso and head could be a body plan. But its reductionist.When I describe a body plan I'm going to more complicated aspects of it. The structure of a particular eye, ear, hip, ligaments, etc., and everything to make them work. All of these are tightly integrated components. They are expressed very early in development. You can only modify them globally and not incrementally. As to ID it's irrelevant. I'm not addressing ID, I'm addressing whether Darwinism is correct.

So? That doesn't mean it's not a transitional structure, or they wouldn't call it a "Transitional mammalian middle ear".

If it already exists you can't transition to it. That's pretty basic.

A transitional fossil is any fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group."

Nice definition, but you can't use it. It assumes Darwinism which is the matter under discussion.

Certainly no one who understands evolution theory, which posits a branching process.

So it's irrelevant.

Each step in the evolutionary process increased hearing function while maintaining jaw function.

There's no proof so far Darwinism is true. So it's just another assumption

They have far more similarities than differences.

Irrelevant. The question is can Darwinian theory explain the differences.

Australopithecus could walk efficiently in the upright position. What's amazing it that the existence of all these sorts of hominines is exactly what we would expect from an evolutionary process.

I'm sorry, you cannot prove that. You have no feet. The pelvis is wrong. The legs bones are wrong. The spine is wrong. All you got is knees that are knocked at a 15 degree angle. Even Orangutans are closer to the human gait than that. And if you look at the latest anatomical model of afarensis you will see a knuckle walking ape.

Okay. We just read it again. Of it's many problems the most egregious is that the paper ignores direct experimental results that show protein folds are common in sequence space

A. Who is we? You have a frog in your pocket? Or is that a royal we?B. Axe and Gauger took the two most similar geneomes, Kbl2 which breaks down threonine and BioF2 which is used to build biotin, and sought to co-opt the function of kbl2 to produce BioF2. They tried single point mutations, multiple point mutations, multiple coordinated mutations, etc. It proved impossible. If you cannot mutate Kbl2 to produce the function of BioF2 then functional protein folds must be exceedingly rare in sequence space.C. The question is not whether there are protein folds or are they common. The question is what are the statistical probabilities of a novel functional protein fold arising. A functional protein fold is that can either perform a function or combine with other proteins to perform a function. Hemoglobin is a functional protein. They are rare in sequence space given the huge numbers of possibilities. This a is what population geneticist do.

You really need to provided proper quotes, links, or citations or something. There's only one previous mention of "Meng" on the thread.

Now on to your confusion. Meng wrote the paper on Liaoconodon hui so if I refer to Meng or Liaoconodon hui the quote is about him or it. Luo wrote the paper on yanoconodon. So if I refer to yanoconodon or Luo I'm refering to him or it. Nature published both papers. You would know this if you'd actually read anything but the title of the paper. I'm not going to lead you around like a child. Follow the argument.

It would help if Darwinist actually read and thought about what the other side had to say. That would help them avoid mischaracterizing the other sides claims. I run into this all the time in theological discussions too. reading rebuttals on pro-Darwinian websites, and Wikipedia falls into this category, without reading the source materials is handing your brain over to someone else.

eklektos: I run into this all the time in theological discussions too. reading rebuttals on pro-Darwinian websites, and Wikipedia falls into this category, without reading the source materials is handing your brain over to someone else.

You appealed to "People who work in the field agree that life requires a F,G, or mid K main sequence star." However, apparently, you completely missed the fact that the majority of the basis for that requirement was for life to evolve, which you don't even believe in the first place.

eklektos: When I describe a body plan I'm going to more complicated aspects of it.

It's not the usual definition, but okay.

eklektos: You can only modify them globally and not incrementally.

You seem to mean that you have to change many things at once if you make a change anywhere. That is not correct. A small change in a single gene can cause coordinated changes throughout the structure. Consider that a slight change in the amount of growth hormone will cause multiple changes. Your feet will still reach the ground.

That's fine, but because you are using a different definition, it can lead to confusion. http://en.wikipedia.org/wiki/Body_plan

eklektos: If it already exists you can't transition to it.

So you're arguing by redefining words?

eklektos: Nice definition, but you can't use it. It assumes Darwinism which is the matter under discussion.

That's the definition. You might argue there is no such thing, like unicorns. But when a scientists says it's transitional, that's what they mean.

eklektos: So it's irrelevant.

It's directly relevant.

eklektos: There's no proof so far Darwinism is true.

It's a testable and tested claim. Each change in the posited transition led to increased hearing ability while maintaining jaw function. In other words, it fits the prediction from Reichert–Gaupp theory. Not bad for a century old theory based on studies of embryos to predict what will be found in the rocks.

eklektos: Irrelevant.

You seem to not understand what that word means. You said "Humans and apes are 'similar' in superficial ways." They have far more similarities than differences, and those similarities are hardly superficial. Do you want a list? A complex cell structure with a nucleus, bilateral symmetry; an alimentary canal, a nerve cord protected by bony vertebrae, a bony head with an array of sense organs, four limbs, four chambered heart, hair, mammary glands, and thousands of other points of similarity. They even have similar blood types.

Evolutionism posits a somewhat gradual, incremental evolution driven by culled genetic accidents. Natural selection, a process of elimination, is said to be blind, mindless and incorporates heritable random, as in happenstance/ accidental, mutations. Dawkins calls it blind watchmaker evolution.

What we need is a way to model what mutations do. That is something beyond the piddly changes we observe. Changes in beak size does not explain the finch. Anti-biotic resistance does not explain bacteria. Moth coloration does not explain the moth. Changes in eye color does not explain the vision system nor the type of eye nor the organism. An albino dwarf with sickle-celled anemia is what we can get when mutations accumulate. Not quite what evolutionism requires.

We need to be able to test the hypothesis that changes to genomes can account for the diversity of life starting from the first populations as Darwin saw it- simple prokaryotes. Only then could we determine if natural selection is up to the task. But thanks to the current state of biology being dominated by blind watchmaker evolution, no one has any idea what makes an organism what it is and the evidence is against the “organisms are the sum of their genome

You would think that answering that question what makes an organism what it is? (with science as opposed to dogmatic declaration) with be paramount to biology. Because without an answer to that question evolutionism is untestable and Dobzhansky is just question begging "Nothing in biology makes sense except in the light of evolution".

And that is another reason why Doug Theobald's "29+ evidences for macroevolution" is absent a mechanism and also why it fails-> there aren't any known mechanisms for producing macroevolutionary change because no one even knows what it entails.

* we are just what emerges from the somehow coordinayed interactions of the matter and energy of a fertilized egg (the environemnet wouldn’t change what type of organism comes out)

Let's go into detail on how the Cleveland Museum assembled it's afarensis model, and why I don't trust evolutionary paleoanthropologists. In the reconstruction they several things. They took a metatarsal found nowhere near an afarensis and assigned it to afarensis. They took two pieces of a hip which fit perfectly together, were at the angle of an ape hip, and remodeled them to fit what they wanted. They took the ribs from another skeleton(big man) 48 kilometers away and added them to their model. But these ribs are barrel shaped like a humans. The ribs actually with the afarensis skeleton(Lucy) are conical. They also took the shoulder blade from big man and assigned them to afarensis even though another afarensis skeleton (Selam) had an apes shoulder blade. They reconstructed the leg from a single leg bone which at the ankle is angled improperly for a bipedal gait. And there you have it, Johnny Cash's Cadillac. The whole reason for this is that they assume that genus Homo didn't "evolve" that early.

If you think this is science then my dog is more scientific than you are.

You seem to mean that you have to change many things at once if you make a change anywhere. That is not correct. A small change in a single gene can cause coordinated changes throughout the structure. Consider that a slight change in the amount of growth hormone will cause multiple changes. Your feet will still reach the ground.

As in the afarensis example you cannot just change the foot. You'd get eaten.

It's directly relevant.

No, it's not. When you find the mythological ancestor you can talk about transitioning. Till then it's an argument from silence. Either you did the implausible twice or you lost function from a transition from a mythological ancestor.

"The results of the analyses reveal that australopithecines and humans uniquely share features of the neural arch and spinal curvature critical for frequent bipedal walking and standing. However, these early hominids have a high incidence of centrum pathology and differ from humans in relative size and proportions of lumbosacral centra, suggesting dissimilarities between modern and early hominids in spinal mechanics. These differences also indicate that evolutionary transformation to habitual bipedality occurred in a mosaic fashion, with lumbar lordosis and vertical stability initially more important than orthograde weight bearing."

That was from the article. So no, it wasn't "habitually bipedal". It was lunch. If you want to look at the actual Vertebrae and note the differences see:

In short the spine is not Homo, and would not support the weight of bipedal gait for any length of time. As it different from apes in a very minute way there is no reason to believe afarensis was a bipedal walker for anything other than short periods, like other apes. And actually the spine is so degraded it is hard to come to any conclusions about it. And there's still the problem of the feet, chest, shoulder blade, legbone, etc.

Right. They tried to evolve a dog into a cat

That's disingenuous. They took two of the most similar genomes and tried to see if it could be mutated to the function of another genome. If this small task could not be accomplished what makes you think it could ever be accomplished? So why would you think any genome could be mutated to another function??? If it can't then you can't co-opt.

Right, and countless researchers have shown that functional proteins are common in sequence space.

You are missing the point. What is you're reference? And given the number of possibilities they are not common. It's not an issue of how many there are, but how many are possible given the possibilities. So to keep repeating this canard is not answering the question.

You seem to think that phylogeny never influences embryonic development, but that's simply not the case.

That's nonsense. It's not "recapitulating" anything. It's performing the specific function that it's encoded for. You can't take a disproven theory and say "well it happens sometimes". Get real.

Furthermore, eukaryotic-only folds were found to be, on average, more designable than prokaryotic-only folds, according to an approximate measure of designability. The second study [71] investigated the relationship between the selection pressure on stability and the ability of a model protein to evolve ligand-binding function. It was found that proteins evolve function more efficiently when the selection pressure on stability is low, and that it is easier to enhance stability while maintaining high function than to enhance function while maintaining high stability.

http://www.sbg.bio.ic.ac.uk/~brj03/papers/default.pdf

So much for ragged teeth, better be velvet gloves. Again, you're talking about designed genes not population genetics...oops

This is despite the fact that methyltransferases have clearly undergone such gene rearrangements in the past, and there is no evidence that lipases have. Clearly, guidelines for which proteins are likely to accept such an operation, and especially which ones are likely to benefit from it by developing new or improved function must still be determined.

Although competent enough to confer antibiotic resistance at a low level, the evolved enzyme is significantly less active on cefotaxime than its role model.

http://www.nature.com/nbt/journal/v24/n3/full/nbt0306-328.html#B5

Degraded function. Hmm...

Here's your favorite source, Wikipedia:

If one possible confirmation was tested every 10/13 second, then it would take about 10/77 years to sample all possible conformations. However, proteins are properly folded within the body on short timescales all the time, meaning that the process cannot be random and, thus, can potentially be modeled.

http://en.wikipedia.org/wiki/De_novo_protein_structure_prediction

Pay attention to the last sentence and see if you can spot the logical error.

However, even with a mutation frequency of m = 22.5, such events were found to be quite rare; among all pre- and postsort clones analyzed, only one mutant (22.5-1) possessed an amino acid change resulting from two base changes in a single codon.

The point is that you're claim that "functional proteins are common in sequence space" is false.

All of the papers describe the attempt to change proteins and they usually lead to decreased function.They aren't as good as momma nature. And she did it by accident. Your not dealing with the issue of frequency of proteins in sequence space. Come on Borg, you've got to do better. Follow the argument

It alters the structure throughout, which you suggested couldn't happen. If you just want to increase the length of limbs, on the other hand, then modify Prx1 expression during development.

You're not changing the fundamental structure of the hand. You're talking about downstream components. And you've said nothing remotely interesting. Dogs come in all sizes, so what?. We are discussing developmental genetic regulatory systems in embryos. Another category error.

Functional proteins are common in sequence space

In conclusion, we suggest that functional proteins are sufficiently common in protein sequence space (roughly 1 in 10/11) that they may be discovered by entirely stochastic means, such as presumably operated when proteins were first used by living organisms. However,this frequency is still low enough to emphasize the magnitude of the problem faced by those attempting de novo protein design.

And they were only looking at whether it would bind to ATP. And there are a great many population geneticist who disagree with even the 10/11 figure. That's the low end. That does not address the whole problem of functionality. Further they were looking at simple proteins, not complex ones. Every time the mutation must affect more base pairs the statistical probability goes up exponentially.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010983/

Yet excitement over the untold riches of sequence space must be tempered by the recognition that the great majority of those sequences don't code for anything interesting; most don't even fold. Estimates for the density of functional proteins in sequence space range anywhere from 1 in 10/12 to 1 in 10/77. No matter how you slice it, proteins are rare. Useful ones are even more rare. This might lead one to believe that discovering new proteins by mutation and selection is highly unlikely and to discount evolution as an algorithm for discovery.

Understanding how functional proteins are distributed in sequence space is fundamental to the success of directed evolution. Another key factor, often ignored, however, is the starting point. Yes, the protein scraped from the bottom of your shoe or collected from your refrigerator is one of those rare sequences that encodes a functional protein. But it is not necessarily a good starting point for obtaining the protein of your dreams.

http://www.nature.com/nbt/journal/v24/n3/full/nbt0306-328.html

Mark that, directed evolution These people are trying to produce them! Nature is mindless. If they are required to assemble something like a flagellar motor then they can't hang about because they will be quickly lost due to fitness cost. So, in the case of the flagellar motor which has 34 complex protein folds, 24 of which are novel so they can't be co-opted, you must generate 24 by de novo mutations, and all at relatively the time, or they will be eliminated.

So stop saying functional protein folds are common in sequence space. because they aren't.

Hey guys, I finally figured out who Zachriel is, he's a class project. So he's a conglomeration of people. Which of course is why he's so deceptive. He's a hive mind. He's the Borg! How could I have been so thick.

Of course there's always the chance he's mentally ill. But I prefer the latter. Zachriel, are you in China? I'd love to go to China. I've been all over Europe, but never to Asia. Toodles

You indicated that you can't make an incremental genetic change with the result of changes throughout the structure. That wasn't true.

I was referring to DRGN's which I thought you'd understood. You should keep up better. You're talking about a peripheral change in the expression of the gene. You're not talking about changing the gene or any higher order developmental network. And if you think evolutionist don't know this you're deluding yourself.

Every discovery creates two more gaps!

Off point.

You probably mean genes, not genomes. Dogs and cats are very similar too.

You're correct, I used the the word for the whole chain. My bad. The similarities are irrelevant, the differences are what must be overcome.

Kbl2 and BioF2 share a common ancestor, just like cats and dogs. But cats didn't evolve into dogs, and Kbl2 didn't evolve into BioF2

First you don't know that. Second the question is can you co-opt the function of a gene to provide a new function. If not then you're just babbling. Third you've made another category error. Kbl2 is a gene, a relatively small gene. For Neo-Darwinism to work it must be able to convert the function of an existing gene to a new function.The rest of your statement is irrelevant. You might need to go assimilate some more people.

There are many references, but one of the first studies was Keefe & Szostak, Functional proteins from a random-sequence library, Nature 2001.

Dudes and Dudettes, I just quoted that, you obviously didn't read it very well.:

In conclusion, we suggest that functional proteins are sufficiently common in protein sequence space (roughly 1 in 10/11) that they may be discovered by entirely stochastic means, such as presumably operated when proteins were First used by living organisms. However, this frequency is still low enough to emphasize the magnitudeof the problem faced by those attempting de novo protein design.

And as I said he's on the low end of the spectrum. Plus that's the simplest protein. Not a complex chain of proteins which must be linked to perform a function. You also left out the qualifier. If you think 10/11 is good odds then I suggest you go spend all your money on lottery tickets. You're sure to win!

Handwaving. The structure was predicted over a century ago based on studies of embryonic development.

A. You don't have a sequence. B. Then it's blind luck. Recapitulation is false. And you don't get to say it's true when it suits you. Either the theory is true or it's false.

Changing the length of the phalanges is changing the structure of the hand. It also directly contradicts your statement above that this can't possibly happen.

eklektos: "However, this frequency is still low enough to emphasize the magnitude of the problem faced by those attempting de novo protein design."

Sure. Protein engineers don't normally have the experimental resources even on the scale of a typical septic tank.

eklektos: And they were only looking at whether it would bind to ATP.

That's right. Other functional proteins have been found, so functional sequences are denser than what a test for a single function would determine.

eklektos: If you think 10/11 is good odds...

There's about a thousand times that many in your gut.

eklektos: So stop saying functional protein folds are common in sequence space. because they aren't.

The minimum frequency is 1 in 10^11.

eklektos: You don't have a sequence.

Every time they find a transitional it means two new gaps!

eklektos: Recapitulation is false.

While embryos don't recapitulate their evolutionary history, many aspects of development reflect their phylogenetic position. That's why a prediction made a century ago, Reichert–Gaupp theory, based on studies of embryos accurately predicted what scientists observe in the rocks.

Changing the length of the phalanges is changing the structure of the hand. It also directly contradicts your statement above that this can't possibly happen

It's still a hand. The morphological structure is unchanged. And we were discussing DGRN's not peripheral systems. You're dodging the issue Borg.

Sure. Protein engineers don't normally have the experimental resources even on the scale of a typical septic tank.

That's too stupid to respond to.

That's right. Other functional proteins have been found, so functional sequences are denser than what a test for a single function would determine.

Those were directed and natural proteins are undirected. The other proteins were inferior, and it was a very simple protein. A more complex protein is exponentially more difficult. You are once again dodging the issue

There's about a thousand times that many in your gut.

So, mutations are happening at 10/11 in your gut is? Borg really? That's not how it works. Are you that clueless? That number is the odds of achieving the de novo fold given the number of trials and population.

The minimum frequency is 1 in 10/11

Even at the lowest frequency it's unlikely for a simple protein. You really don't have a clue what you're talking about. You're also still dodging the issue.

That's why a prediction made a century ago, Reichert–Gaupp theory, based on studies of embryos accurately predicted what scientists observe in the rocks.

Ad hoc logic, which is what you're using. "It looks similar so it's recapitulating it's evolutionary history.

the minimum frequency is nowhere near 1 in 10^11. That was just the frequency of sequences that stuck to ATP. That means nothing now that we can actually see how ATP is powering the machinery in cells. That's like saying that when I throw gasoline at my car and some of it sticks, that we're one step away from injecting it into an internal combustion engine and generating power.

I totally agree. But even that number remarkably high. And that is just for de novo generation of a floppy chain in particular very simple protein. Not a functional protein that could be used for something. So functional proteins are not common in sequence space. But Borg doesn't seem to be able to connect the dots.

No single confirmation is sufficient to "prove" a theory, but the more confirmations, the more types of confirmations, the more surprising the confirmations, the stronger our confidence will be in the hypothesis. But all hypotheses are considered tentative, and most hypotheses are modified at some point no matter how strongly supported.

I'll try this one last time. Given the number of trials available in a given time and given the population available the odds for each attempt is 10/11 on the low end. That is the odds for each trial throughout the history of life. This is why de novo protein design by random chance is problematic. If you have to have a three base pair change you're approaching the age of life on earth. If you have to have a 4 base pair change you're approaching the age of the earth. Have to change 5 base pairs and you're statistical probability is zero. There's not enough time or population available. Not only that you have to have do that with a great many proteins which must be usable quickly. To build a flagellar motor you have to have 24 novel protein folds which cannot be co-opted, they don't exist except in the motor. You must have them all quickly or they will be destroyed and reused due to fitness cost. Without the whole assembly the motor will not work so the bacteria will be selected out. And this is using the lowest probability. The actual probability is likely far higher. So Neo-Darwinian concept of co-option is being abandon. If you don't get it yet you never will.

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/